Variant report

Variant	rs28497454
Chromosome Location	chr4:26907852-26907853
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26894419..26896877-chr4:26907421..26910331,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11729927	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11730235	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11734308	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11737218	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11943948	0.87[ASN][1000 genomes]
rs12641261	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12644073	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12646473	0.91[ASN][1000 genomes]
rs12650172	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13116341	0.81[ASN][1000 genomes]
rs13138942	0.89[ASN][1000 genomes]
rs13139464	0.83[ASN][1000 genomes]
rs28520489	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34996346	0.89[ASN][1000 genomes]
rs3792685	0.91[ASN][1000 genomes]
rs3924178	0.81[ASN][1000 genomes]
rs4274829	0.87[ASN][1000 genomes]
rs4407490	0.80[ASN][1000 genomes]
rs4505809	0.89[ASN][1000 genomes]
rs4519790	0.87[ASN][1000 genomes]
rs4532223	0.87[ASN][1000 genomes]
rs4557250	0.87[ASN][1000 genomes]
rs4557251	0.87[ASN][1000 genomes]
rs57663175	0.99[ASN][1000 genomes]
rs57686546	0.98[ASN][1000 genomes]
rs58075729	0.80[ASN][1000 genomes]
rs58968032	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60890366	0.95[ASN][1000 genomes]
rs61047003	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62302532	0.93[ASN][1000 genomes]
rs62302533	0.93[ASN][1000 genomes]
rs62302535	0.92[ASN][1000 genomes]
rs6448479	0.88[ASN][1000 genomes]
rs6448484	0.89[ASN][1000 genomes]
rs6448488	0.93[ASN][1000 genomes]
rs6815719	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833053	0.93[ASN][1000 genomes]
rs6833895	0.88[ASN][1000 genomes]
rs6835631	0.95[ASN][1000 genomes]
rs6844153	0.95[ASN][1000 genomes]
rs6853032	0.88[ASN][1000 genomes]
rs73116683	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs73811400	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73813220	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7655686	0.96[ASN][1000 genomes]
rs9790789	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1000568	chr4:26886920-27049554	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28497454	STIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26880600-26921600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:26886600-26921600	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:26898400-26914400	Weak transcription	HSMM	muscle
4	chr4:26899400-26908000	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr4:26900400-26913200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:26900800-26908000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr4:26901800-26909000	Weak transcription	GM12878-XiMat	blood
8	chr4:26902600-26909000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:26902800-26908800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr4:26902800-26909400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:26902800-26909400	Weak transcription	Brain Substantia Nigra	brain
12	chr4:26902800-26909800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr4:26902800-26912400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr4:26902800-26914400	Weak transcription	Right Atrium	heart
15	chr4:26903000-26913000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr4:26903600-26909000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr4:26904400-26910200	Weak transcription	Pancreas	Pancrea
18	chr4:26904400-26913800	Weak transcription	Left Ventricle	heart
19	chr4:26904800-26909000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr4:26905000-26910400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:26905200-26909200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr4:26906000-26910600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr4:26906400-26909200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr4:26906800-26909000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:26906800-26909000	Weak transcription	Adipose Nuclei	Adipose
26	chr4:26906800-26909400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:26906800-26909400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:26906800-26912000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr4:26907000-26909000	Weak transcription	Brain Angular Gyrus	brain
30	chr4:26907000-26909000	Weak transcription	Brain Anterior Caudate	brain
31	chr4:26907000-26909000	Weak transcription	Brain Hippocampus Middle	brain
32	chr4:26907000-26909000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr4:26907000-26909400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr4:26907000-26909400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:26907000-26909400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:26907000-26909800	Weak transcription	Ovary	ovary
37	chr4:26907000-26913000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:26907000-26913200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:26907000-26914400	Weak transcription	Psoas Muscle	Psoas
40	chr4:26907000-26917400	Weak transcription	Gastric	stomach
41	chr4:26907200-26908600	Weak transcription	Primary B cells from cord blood	blood
42	chr4:26907200-26908600	Weak transcription	Primary T cells from cord blood	blood
43	chr4:26907200-26909000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr4:26907200-26909000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr4:26907200-26909000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:26907200-26909200	Weak transcription	Fetal Lung	lung
47	chr4:26907200-26909400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr4:26907200-26909400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr4:26907200-26909400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr4:26907200-26909400	Weak transcription	Brain Inferior Temporal Lobe	brain

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